data_2YGP # _entry.id 2YGP # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.329 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2YGP PDBE EBI-48078 WWPDB D_1290048078 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 2YGQ unspecified ;WIF DOMAIN-EPIDERMAL GROWTH FACTOR (EGF)-LIKE DOMAINS 1-3 OF HUMAN WNT INHIBITORY FACTOR 1 IN COMPLEX WITH 1,2-DIPALMITOYLPHOSPHATIDYLCHOLINE ; PDB 2YGO unspecified 'WIF DOMAIN-EGF-LIKE DOMAIN 1 OF HUMAN WNT INHIBITORY FACTOR 1 IN COMPLEX WITH 1,2- DIPALMITOYLPHOSPHATIDYLCHOLINE' PDB 2YGN unspecified 'WIF DOMAIN OF HUMAN WNT INHIBITORY FACTOR 1 IN COMPLEX WITH 1,2-DIPALMITOYLPHOSPHATIDYLCHOLINE' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2YGP _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2011-04-19 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Malinauskas, T.' 1 'Aricescu, A.R.' 2 'Lu, W.' 3 'Siebold, C.' 4 'Jones, E.Y.' 5 # _citation.id primary _citation.title 'Modular Mechanism of Wnt Signaling Inhibition by Wnt Inhibitory Factor 1' _citation.journal_abbrev Nat.Struct.Mol.Biol. _citation.journal_volume 18 _citation.page_first 886 _citation.page_last ? _citation.year 2011 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1545-9993 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21743455 _citation.pdbx_database_id_DOI 10.1038/NSMB.2081 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Malinauskas, T.' 1 ? primary 'Aricescu, A.R.' 2 ? primary 'Lu, W.' 3 ? primary 'Siebold, C.' 4 ? primary 'Jones, E.Y.' 5 ? # _cell.entry_id 2YGP _cell.length_a 50.760 _cell.length_b 134.241 _cell.length_c 60.193 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YGP _symmetry.space_group_name_H-M 'C 2 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 21 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'WNT INHIBITORY FACTOR 1' 21131.082 1 ? YES 'WIF DOMAIN-EGF-LIKE DOMAIN 1, RESIDUES 35-210' ? 2 non-polymer syn 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE 734.039 1 ? ? ? ? 3 non-polymer man 2-acetamido-2-deoxy-beta-D-glucopyranose 221.208 1 ? ? ? ? 4 non-polymer syn 'CALCIUM ION' 40.078 1 ? ? ? ? 5 non-polymer syn SPERMIDINE 145.246 1 ? ? ? ? 6 water nat water 18.015 111 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name WIF-1 # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;ETGSLYLWIDAHQARVLIGFEEDILIVSEG(MLY)MAPFTHDFR(MLY)AQQRWPAIPVNIHSMNFTWQAAGQAEYFYEF LSLRSLD(MLY)GIMADPTVNVPLLGTVPH(MLY)ASVVQVGFPCLG(MLY)QDGVAAFEVDVIVMNSEGNTIL(MLY)T PQNAIFFKTCQQAECPGGCRNGGFCNERRICECPDGFHGPHCEGTKHHHHHH ; _entity_poly.pdbx_seq_one_letter_code_can ;ETGSLYLWIDAHQARVLIGFEEDILIVSEGKMAPFTHDFRKAQQRWPAIPVNIHSMNFTWQAAGQAEYFYEFLSLRSLDK GIMADPTVNVPLLGTVPHKASVVQVGFPCLGKQDGVAAFEVDVIVMNSEGNTILKTPQNAIFFKTCQQAECPGGCRNGGF CNERRICECPDGFHGPHCEGTKHHHHHH ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLU n 1 2 THR n 1 3 GLY n 1 4 SER n 1 5 LEU n 1 6 TYR n 1 7 LEU n 1 8 TRP n 1 9 ILE n 1 10 ASP n 1 11 ALA n 1 12 HIS n 1 13 GLN n 1 14 ALA n 1 15 ARG n 1 16 VAL n 1 17 LEU n 1 18 ILE n 1 19 GLY n 1 20 PHE n 1 21 GLU n 1 22 GLU n 1 23 ASP n 1 24 ILE n 1 25 LEU n 1 26 ILE n 1 27 VAL n 1 28 SER n 1 29 GLU n 1 30 GLY n 1 31 MLY n 1 32 MET n 1 33 ALA n 1 34 PRO n 1 35 PHE n 1 36 THR n 1 37 HIS n 1 38 ASP n 1 39 PHE n 1 40 ARG n 1 41 MLY n 1 42 ALA n 1 43 GLN n 1 44 GLN n 1 45 ARG n 1 46 TRP n 1 47 PRO n 1 48 ALA n 1 49 ILE n 1 50 PRO n 1 51 VAL n 1 52 ASN n 1 53 ILE n 1 54 HIS n 1 55 SER n 1 56 MET n 1 57 ASN n 1 58 PHE n 1 59 THR n 1 60 TRP n 1 61 GLN n 1 62 ALA n 1 63 ALA n 1 64 GLY n 1 65 GLN n 1 66 ALA n 1 67 GLU n 1 68 TYR n 1 69 PHE n 1 70 TYR n 1 71 GLU n 1 72 PHE n 1 73 LEU n 1 74 SER n 1 75 LEU n 1 76 ARG n 1 77 SER n 1 78 LEU n 1 79 ASP n 1 80 MLY n 1 81 GLY n 1 82 ILE n 1 83 MET n 1 84 ALA n 1 85 ASP n 1 86 PRO n 1 87 THR n 1 88 VAL n 1 89 ASN n 1 90 VAL n 1 91 PRO n 1 92 LEU n 1 93 LEU n 1 94 GLY n 1 95 THR n 1 96 VAL n 1 97 PRO n 1 98 HIS n 1 99 MLY n 1 100 ALA n 1 101 SER n 1 102 VAL n 1 103 VAL n 1 104 GLN n 1 105 VAL n 1 106 GLY n 1 107 PHE n 1 108 PRO n 1 109 CYS n 1 110 LEU n 1 111 GLY n 1 112 MLY n 1 113 GLN n 1 114 ASP n 1 115 GLY n 1 116 VAL n 1 117 ALA n 1 118 ALA n 1 119 PHE n 1 120 GLU n 1 121 VAL n 1 122 ASP n 1 123 VAL n 1 124 ILE n 1 125 VAL n 1 126 MET n 1 127 ASN n 1 128 SER n 1 129 GLU n 1 130 GLY n 1 131 ASN n 1 132 THR n 1 133 ILE n 1 134 LEU n 1 135 MLY n 1 136 THR n 1 137 PRO n 1 138 GLN n 1 139 ASN n 1 140 ALA n 1 141 ILE n 1 142 PHE n 1 143 PHE n 1 144 LYS n 1 145 THR n 1 146 CYS n 1 147 GLN n 1 148 GLN n 1 149 ALA n 1 150 GLU n 1 151 CYS n 1 152 PRO n 1 153 GLY n 1 154 GLY n 1 155 CYS n 1 156 ARG n 1 157 ASN n 1 158 GLY n 1 159 GLY n 1 160 PHE n 1 161 CYS n 1 162 ASN n 1 163 GLU n 1 164 ARG n 1 165 ARG n 1 166 ILE n 1 167 CYS n 1 168 GLU n 1 169 CYS n 1 170 PRO n 1 171 ASP n 1 172 GLY n 1 173 PHE n 1 174 HIS n 1 175 GLY n 1 176 PRO n 1 177 HIS n 1 178 CYS n 1 179 GLU n 1 180 GLY n 1 181 THR n 1 182 LYS n 1 183 HIS n 1 184 HIS n 1 185 HIS n 1 186 HIS n 1 187 HIS n 1 188 HIS n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name HUMAN _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'HOMO SAPIENS' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name HUMAN _entity_src_gen.pdbx_host_org_scientific_name 'HOMO SAPIENS' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 9606 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line 'N-ACETYLGLUCOSAMINYLTRANSFERASE I-NEGATIVE HEK 293S GNTI(-)CELLS' _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type PLASMID _entity_src_gen.pdbx_host_org_vector PHLSEC _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code WIF1_HUMAN _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession Q9Y5W5 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2YGP _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 4 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 179 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q9Y5W5 _struct_ref_seq.db_align_beg 35 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 210 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 35 _struct_ref_seq.pdbx_auth_seq_align_end 210 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 2YGP GLU A 1 ? UNP Q9Y5W5 ? ? 'expression tag' 32 1 1 2YGP THR A 2 ? UNP Q9Y5W5 ? ? 'expression tag' 33 2 1 2YGP GLY A 3 ? UNP Q9Y5W5 ? ? 'expression tag' 34 3 1 2YGP TRP A 46 ? UNP Q9Y5W5 MET 77 'engineered mutation' 77 4 1 2YGP MLY A 135 ? UNP Q9Y5W5 GLN 166 variant 166 5 1 2YGP GLY A 180 ? UNP Q9Y5W5 ? ? 'expression tag' 211 6 1 2YGP THR A 181 ? UNP Q9Y5W5 ? ? 'expression tag' 212 7 1 2YGP LYS A 182 ? UNP Q9Y5W5 ? ? 'expression tag' 213 8 1 2YGP HIS A 183 ? UNP Q9Y5W5 ? ? 'expression tag' 214 9 1 2YGP HIS A 184 ? UNP Q9Y5W5 ? ? 'expression tag' 215 10 1 2YGP HIS A 185 ? UNP Q9Y5W5 ? ? 'expression tag' 216 11 1 2YGP HIS A 186 ? UNP Q9Y5W5 ? ? 'expression tag' 217 12 1 2YGP HIS A 187 ? UNP Q9Y5W5 ? ? 'expression tag' 218 13 1 2YGP HIS A 188 ? UNP Q9Y5W5 ? ? 'expression tag' 219 14 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CA non-polymer . 'CALCIUM ION' ? 'Ca 2' 40.078 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 MLY 'L-peptide linking' n N-DIMETHYL-LYSINE ? 'C8 H18 N2 O2' 174.241 NAG 'D-saccharide, beta linking' . 2-acetamido-2-deoxy-beta-D-glucopyranose ? 'C8 H15 N O6' 221.208 PCF non-polymer . 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE ? 'C40 H80 N O8 P' 734.039 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 SPD non-polymer . SPERMIDINE 'N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34)' 'C7 H19 N3' 145.246 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 2YGP _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.29 _exptl_crystal.density_percent_sol 50 _exptl_crystal.description NONE # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '1.1 M DIAMMONIUM TARTRATE, PH 7.0, 20 MM SPERMIDINE, 0.5 MM CACL2' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.978 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'DIAMOND BEAMLINE I24' _diffrn_source.pdbx_synchrotron_site Diamond _diffrn_source.pdbx_synchrotron_beamline I24 _diffrn_source.pdbx_wavelength 0.978 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2YGP _reflns.observed_criterion_sigma_I 0.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 29.32 _reflns.d_resolution_high 2.22 _reflns.number_obs 10433 _reflns.number_all ? _reflns.percent_possible_obs 99.4 _reflns.pdbx_Rmerge_I_obs 0.09 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 12.70 _reflns.B_iso_Wilson_estimate 35.19 _reflns.pdbx_redundancy 6.4 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 2.22 _reflns_shell.d_res_low 2.28 _reflns_shell.percent_possible_all 92.0 _reflns_shell.Rmerge_I_obs 0.57 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.30 _reflns_shell.pdbx_redundancy 6.0 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2YGP _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 10431 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 29.316 _refine.ls_d_res_high 2.222 _refine.ls_percent_reflns_obs 99.33 _refine.ls_R_factor_obs 0.1875 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1855 _refine.ls_R_factor_R_free 0.2289 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.8 _refine.ls_number_reflns_R_free 502 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 51.04 _refine.aniso_B[1][1] 8.8036 _refine.aniso_B[2][2] -7.9788 _refine.aniso_B[3][3] -0.8248 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.365 _refine.solvent_model_param_bsol 55.777 _refine.pdbx_solvent_vdw_probe_radii 0.90 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.61 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.33 _refine.pdbx_overall_phase_error 21.66 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1406 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 75 _refine_hist.number_atoms_solvent 111 _refine_hist.number_atoms_total 1592 _refine_hist.d_res_high 2.222 _refine_hist.d_res_low 29.316 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function f_bond_d 0.015 ? ? 1520 'X-RAY DIFFRACTION' ? f_angle_d 2.217 ? ? 2037 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 19.537 ? ? 587 'X-RAY DIFFRACTION' ? f_chiral_restr 0.149 ? ? 214 'X-RAY DIFFRACTION' ? f_plane_restr 0.009 ? ? 255 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all 'X-RAY DIFFRACTION' . 2.2220 2.4455 2363 0.2499 97.00 0.2946 . . 127 . . 'X-RAY DIFFRACTION' . 2.4455 2.7991 2455 0.2071 100.00 0.2949 . . 134 . . 'X-RAY DIFFRACTION' . 2.7991 3.5256 2501 0.1687 100.00 0.1966 . . 120 . . 'X-RAY DIFFRACTION' . 3.5256 29.3189 2610 0.1747 100.00 0.2093 . . 121 . . # _struct.entry_id 2YGP _struct.title 'WIF domain-EGF-like domain 1 Met77Trp of human Wnt inhibitory factor 1 in complex with 1,2-dipalmitoylphosphatidylcholine' _struct.pdbx_descriptor 'WNT INHIBITORY FACTOR 1' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2YGP _struct_keywords.pdbx_keywords 'SIGNALING PROTEIN' _struct_keywords.text 'SIGNALING PROTEIN, WNT SIGNALING PATHWAY, WNT ANTAGONIST, MORPHOGEN, CANCER, GLYCOSAMINOGLYCAN' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 5 ? F N N 6 ? # _struct_biol.id 1 # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 ASP A 10 ? GLY A 19 ? ASP A 41 GLY A 50 1 ? 10 HELX_P HELX_P2 2 PRO A 34 ? HIS A 37 ? PRO A 65 HIS A 68 5 ? 4 HELX_P HELX_P3 3 ASP A 38 ? GLN A 44 ? ASP A 69 GLN A 75 1 ? 7 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role disulf1 disulf ? ? A CYS 109 SG ? ? ? 1_555 A CYS 146 SG ? ? A CYS 140 A CYS 177 1_555 ? ? ? ? ? ? ? 2.040 ? ? disulf2 disulf ? ? A CYS 151 SG ? ? ? 1_555 A CYS 161 SG ? ? A CYS 182 A CYS 192 1_555 ? ? ? ? ? ? ? 2.033 ? ? disulf3 disulf ? ? A CYS 155 SG ? ? ? 1_555 A CYS 167 SG ? ? A CYS 186 A CYS 198 1_555 ? ? ? ? ? ? ? 2.033 ? ? disulf4 disulf ? ? A CYS 169 SG ? ? ? 1_555 A CYS 178 SG ? ? A CYS 200 A CYS 209 1_555 ? ? ? ? ? ? ? 2.033 ? ? covale1 covale both ? A GLY 30 C ? ? ? 1_555 A MLY 31 N ? ? A GLY 61 A MLY 62 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale2 covale both ? A MLY 31 C ? ? ? 1_555 A MET 32 N ? ? A MLY 62 A MET 63 1_555 ? ? ? ? ? ? ? 1.349 ? ? covale3 covale both ? A ARG 40 C ? ? ? 1_555 A MLY 41 N ? ? A ARG 71 A MLY 72 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale4 covale both ? A MLY 41 C ? ? ? 1_555 A ALA 42 N ? ? A MLY 72 A ALA 73 1_555 ? ? ? ? ? ? ? 1.348 ? ? covale5 covale one ? A ASN 57 ND2 ? ? ? 1_555 C NAG . C1 ? ? A ASN 88 A NAG 1214 1_555 ? ? ? ? ? ? ? 1.431 ? N-Glycosylation covale6 covale both ? A ASP 79 C ? ? ? 1_555 A MLY 80 N ? ? A ASP 110 A MLY 111 1_555 ? ? ? ? ? ? ? 1.345 ? ? covale7 covale both ? A MLY 80 C ? ? ? 1_555 A GLY 81 N ? ? A MLY 111 A GLY 112 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale8 covale both ? A HIS 98 C ? ? ? 1_555 A MLY 99 N ? ? A HIS 129 A MLY 130 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale9 covale both ? A MLY 99 C ? ? ? 1_555 A ALA 100 N ? ? A MLY 130 A ALA 131 1_555 ? ? ? ? ? ? ? 1.356 ? ? covale10 covale both ? A GLY 111 C ? ? ? 1_555 A MLY 112 N ? ? A GLY 142 A MLY 143 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale11 covale both ? A MLY 112 C ? ? ? 1_555 A GLN 113 N ? ? A MLY 143 A GLN 144 1_555 ? ? ? ? ? ? ? 1.376 ? ? covale12 covale both ? A LEU 134 C ? ? ? 1_555 A MLY 135 N ? ? A LEU 165 A MLY 166 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale13 covale both ? A MLY 135 C ? ? ? 1_555 A THR 136 N ? ? A MLY 166 A THR 167 1_555 ? ? ? ? ? ? ? 1.340 ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA ? 6 ? AB ? 4 ? AC ? 4 ? AD ? 2 ? AE ? 2 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA 1 2 ? anti-parallel AA 2 3 ? anti-parallel AA 3 4 ? anti-parallel AA 4 5 ? anti-parallel AA 5 6 ? anti-parallel AB 1 2 ? anti-parallel AB 2 3 ? anti-parallel AB 3 4 ? anti-parallel AC 1 2 ? anti-parallel AC 2 3 ? anti-parallel AC 3 4 ? anti-parallel AD 1 2 ? anti-parallel AE 1 2 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA 1 MLY A 31 ? MET A 32 ? MLY A 62 MET A 63 AA 2 ILE A 24 ? SER A 28 ? ILE A 55 SER A 59 AA 3 LEU A 5 ? ILE A 9 ? LEU A 36 ILE A 40 AA 4 SER A 55 ? ALA A 62 ? SER A 86 ALA A 93 AA 5 SER A 101 ? GLY A 106 ? SER A 132 GLY A 137 AA 6 THR A 87 ? VAL A 88 ? THR A 118 VAL A 119 AB 1 LEU A 93 ? THR A 95 ? LEU A 124 THR A 126 AB 2 TYR A 68 ? SER A 77 ? TYR A 99 SER A 108 AB 3 GLY A 115 ? ASN A 127 ? GLY A 146 ASN A 158 AB 4 THR A 132 ? MLY A 135 ? THR A 163 MLY A 166 AC 1 LEU A 93 ? THR A 95 ? LEU A 124 THR A 126 AC 2 TYR A 68 ? SER A 77 ? TYR A 99 SER A 108 AC 3 GLY A 115 ? ASN A 127 ? GLY A 146 ASN A 158 AC 4 PHE A 142 ? CYS A 146 ? PHE A 173 CYS A 177 AD 1 THR A 132 ? MLY A 135 ? THR A 163 MLY A 166 AD 2 GLY A 115 ? ASN A 127 ? GLY A 146 ASN A 158 AE 1 PHE A 160 ? CYS A 161 ? PHE A 191 CYS A 192 AE 2 CYS A 167 ? GLU A 168 ? CYS A 198 GLU A 199 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA 1 2 N MLY A 31 ? N MLY A 62 O SER A 28 ? O SER A 59 AA 2 3 N ILE A 26 ? N ILE A 57 O LEU A 7 ? O LEU A 38 AA 3 4 N TRP A 8 ? N TRP A 39 O THR A 59 ? O THR A 90 AA 4 5 N TRP A 60 ? N TRP A 91 O SER A 101 ? O SER A 132 AA 5 6 N GLY A 106 ? N GLY A 137 O THR A 87 ? O THR A 118 AB 1 2 N GLY A 94 ? N GLY A 125 O TYR A 70 ? O TYR A 101 AB 2 3 N ARG A 76 ? N ARG A 107 O GLU A 120 ? O GLU A 151 AB 3 4 O VAL A 125 ? O VAL A 156 N ILE A 133 ? N ILE A 164 AC 1 2 N GLY A 94 ? N GLY A 125 O TYR A 70 ? O TYR A 101 AC 2 3 N ARG A 76 ? N ARG A 107 O GLU A 120 ? O GLU A 151 AC 3 4 N PHE A 119 ? N PHE A 150 O PHE A 142 ? O PHE A 173 AD 1 2 N ILE A 133 ? N ILE A 164 O VAL A 125 ? O VAL A 156 AE 1 2 N PHE A 160 ? N PHE A 191 O GLU A 168 ? O GLU A 199 # _database_PDB_matrix.entry_id 2YGP _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 2YGP _atom_sites.fract_transf_matrix[1][1] 0.019701 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.007449 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.016613 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C CA N O P S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLU 1 32 ? ? ? A . n A 1 2 THR 2 33 33 THR THR A . n A 1 3 GLY 3 34 34 GLY GLY A . n A 1 4 SER 4 35 35 SER SER A . n A 1 5 LEU 5 36 36 LEU LEU A . n A 1 6 TYR 6 37 37 TYR TYR A . n A 1 7 LEU 7 38 38 LEU LEU A . n A 1 8 TRP 8 39 39 TRP TRP A . n A 1 9 ILE 9 40 40 ILE ILE A . n A 1 10 ASP 10 41 41 ASP ASP A . n A 1 11 ALA 11 42 42 ALA ALA A . n A 1 12 HIS 12 43 43 HIS HIS A . n A 1 13 GLN 13 44 44 GLN GLN A . n A 1 14 ALA 14 45 45 ALA ALA A . n A 1 15 ARG 15 46 46 ARG ARG A . n A 1 16 VAL 16 47 47 VAL VAL A . n A 1 17 LEU 17 48 48 LEU LEU A . n A 1 18 ILE 18 49 49 ILE ILE A . n A 1 19 GLY 19 50 50 GLY GLY A . n A 1 20 PHE 20 51 51 PHE PHE A . n A 1 21 GLU 21 52 52 GLU GLU A . n A 1 22 GLU 22 53 53 GLU GLU A . n A 1 23 ASP 23 54 54 ASP ASP A . n A 1 24 ILE 24 55 55 ILE ILE A . n A 1 25 LEU 25 56 56 LEU LEU A . n A 1 26 ILE 26 57 57 ILE ILE A . n A 1 27 VAL 27 58 58 VAL VAL A . n A 1 28 SER 28 59 59 SER SER A . n A 1 29 GLU 29 60 60 GLU GLU A . n A 1 30 GLY 30 61 61 GLY GLY A . n A 1 31 MLY 31 62 62 MLY MLY A . n A 1 32 MET 32 63 63 MET MET A . n A 1 33 ALA 33 64 64 ALA ALA A . n A 1 34 PRO 34 65 65 PRO PRO A . n A 1 35 PHE 35 66 66 PHE PHE A . n A 1 36 THR 36 67 67 THR THR A . n A 1 37 HIS 37 68 68 HIS HIS A . n A 1 38 ASP 38 69 69 ASP ASP A . n A 1 39 PHE 39 70 70 PHE PHE A . n A 1 40 ARG 40 71 71 ARG ARG A . n A 1 41 MLY 41 72 72 MLY MLY A . n A 1 42 ALA 42 73 73 ALA ALA A . n A 1 43 GLN 43 74 74 GLN GLN A . n A 1 44 GLN 44 75 75 GLN GLN A . n A 1 45 ARG 45 76 76 ARG ARG A . n A 1 46 TRP 46 77 77 TRP TRP A . n A 1 47 PRO 47 78 78 PRO PRO A . n A 1 48 ALA 48 79 79 ALA ALA A . n A 1 49 ILE 49 80 80 ILE ILE A . n A 1 50 PRO 50 81 81 PRO PRO A . n A 1 51 VAL 51 82 82 VAL VAL A . n A 1 52 ASN 52 83 83 ASN ASN A . n A 1 53 ILE 53 84 84 ILE ILE A . n A 1 54 HIS 54 85 85 HIS HIS A . n A 1 55 SER 55 86 86 SER SER A . n A 1 56 MET 56 87 87 MET MET A . n A 1 57 ASN 57 88 88 ASN ASN A . n A 1 58 PHE 58 89 89 PHE PHE A . n A 1 59 THR 59 90 90 THR THR A . n A 1 60 TRP 60 91 91 TRP TRP A . n A 1 61 GLN 61 92 92 GLN GLN A . n A 1 62 ALA 62 93 93 ALA ALA A . n A 1 63 ALA 63 94 94 ALA ALA A . n A 1 64 GLY 64 95 95 GLY GLY A . n A 1 65 GLN 65 96 96 GLN GLN A . n A 1 66 ALA 66 97 97 ALA ALA A . n A 1 67 GLU 67 98 98 GLU GLU A . n A 1 68 TYR 68 99 99 TYR TYR A . n A 1 69 PHE 69 100 100 PHE PHE A . n A 1 70 TYR 70 101 101 TYR TYR A . n A 1 71 GLU 71 102 102 GLU GLU A . n A 1 72 PHE 72 103 103 PHE PHE A . n A 1 73 LEU 73 104 104 LEU LEU A . n A 1 74 SER 74 105 105 SER SER A . n A 1 75 LEU 75 106 106 LEU LEU A . n A 1 76 ARG 76 107 107 ARG ARG A . n A 1 77 SER 77 108 108 SER SER A . n A 1 78 LEU 78 109 109 LEU LEU A . n A 1 79 ASP 79 110 110 ASP ASP A . n A 1 80 MLY 80 111 111 MLY MLY A . n A 1 81 GLY 81 112 112 GLY GLY A . n A 1 82 ILE 82 113 113 ILE ILE A . n A 1 83 MET 83 114 114 MET MET A . n A 1 84 ALA 84 115 115 ALA ALA A . n A 1 85 ASP 85 116 116 ASP ASP A . n A 1 86 PRO 86 117 117 PRO PRO A . n A 1 87 THR 87 118 118 THR THR A . n A 1 88 VAL 88 119 119 VAL VAL A . n A 1 89 ASN 89 120 120 ASN ASN A . n A 1 90 VAL 90 121 121 VAL VAL A . n A 1 91 PRO 91 122 122 PRO PRO A . n A 1 92 LEU 92 123 123 LEU LEU A . n A 1 93 LEU 93 124 124 LEU LEU A . n A 1 94 GLY 94 125 125 GLY GLY A . n A 1 95 THR 95 126 126 THR THR A . n A 1 96 VAL 96 127 127 VAL VAL A . n A 1 97 PRO 97 128 128 PRO PRO A . n A 1 98 HIS 98 129 129 HIS HIS A . n A 1 99 MLY 99 130 130 MLY MLY A . n A 1 100 ALA 100 131 131 ALA ALA A . n A 1 101 SER 101 132 132 SER SER A . n A 1 102 VAL 102 133 133 VAL VAL A . n A 1 103 VAL 103 134 134 VAL VAL A . n A 1 104 GLN 104 135 135 GLN GLN A . n A 1 105 VAL 105 136 136 VAL VAL A . n A 1 106 GLY 106 137 137 GLY GLY A . n A 1 107 PHE 107 138 138 PHE PHE A . n A 1 108 PRO 108 139 139 PRO PRO A . n A 1 109 CYS 109 140 140 CYS CYS A . n A 1 110 LEU 110 141 141 LEU LEU A . n A 1 111 GLY 111 142 142 GLY GLY A . n A 1 112 MLY 112 143 143 MLY MLY A . n A 1 113 GLN 113 144 144 GLN GLN A . n A 1 114 ASP 114 145 145 ASP ASP A . n A 1 115 GLY 115 146 146 GLY GLY A . n A 1 116 VAL 116 147 147 VAL VAL A . n A 1 117 ALA 117 148 148 ALA ALA A . n A 1 118 ALA 118 149 149 ALA ALA A . n A 1 119 PHE 119 150 150 PHE PHE A . n A 1 120 GLU 120 151 151 GLU GLU A . n A 1 121 VAL 121 152 152 VAL VAL A . n A 1 122 ASP 122 153 153 ASP ASP A . n A 1 123 VAL 123 154 154 VAL VAL A . n A 1 124 ILE 124 155 155 ILE ILE A . n A 1 125 VAL 125 156 156 VAL VAL A . n A 1 126 MET 126 157 157 MET MET A . n A 1 127 ASN 127 158 158 ASN ASN A . n A 1 128 SER 128 159 159 SER SER A . n A 1 129 GLU 129 160 160 GLU GLU A . n A 1 130 GLY 130 161 161 GLY GLY A . n A 1 131 ASN 131 162 162 ASN ASN A . n A 1 132 THR 132 163 163 THR THR A . n A 1 133 ILE 133 164 164 ILE ILE A . n A 1 134 LEU 134 165 165 LEU LEU A . n A 1 135 MLY 135 166 166 MLY MLY A . n A 1 136 THR 136 167 167 THR THR A . n A 1 137 PRO 137 168 168 PRO PRO A . n A 1 138 GLN 138 169 169 GLN GLN A . n A 1 139 ASN 139 170 170 ASN ASN A . n A 1 140 ALA 140 171 171 ALA ALA A . n A 1 141 ILE 141 172 172 ILE ILE A . n A 1 142 PHE 142 173 173 PHE PHE A . n A 1 143 PHE 143 174 174 PHE PHE A . n A 1 144 LYS 144 175 175 LYS LYS A . n A 1 145 THR 145 176 176 THR THR A . n A 1 146 CYS 146 177 177 CYS CYS A . n A 1 147 GLN 147 178 178 GLN GLN A . n A 1 148 GLN 148 179 179 GLN GLN A . n A 1 149 ALA 149 180 180 ALA ALA A . n A 1 150 GLU 150 181 181 GLU GLU A . n A 1 151 CYS 151 182 182 CYS CYS A . n A 1 152 PRO 152 183 183 PRO PRO A . n A 1 153 GLY 153 184 184 GLY GLY A . n A 1 154 GLY 154 185 185 GLY GLY A . n A 1 155 CYS 155 186 186 CYS CYS A . n A 1 156 ARG 156 187 187 ARG ARG A . n A 1 157 ASN 157 188 188 ASN ASN A . n A 1 158 GLY 158 189 189 GLY GLY A . n A 1 159 GLY 159 190 190 GLY GLY A . n A 1 160 PHE 160 191 191 PHE PHE A . n A 1 161 CYS 161 192 192 CYS CYS A . n A 1 162 ASN 162 193 193 ASN ASN A . n A 1 163 GLU 163 194 194 GLU GLU A . n A 1 164 ARG 164 195 195 ARG ARG A . n A 1 165 ARG 165 196 196 ARG ARG A . n A 1 166 ILE 166 197 197 ILE ILE A . n A 1 167 CYS 167 198 198 CYS CYS A . n A 1 168 GLU 168 199 199 GLU GLU A . n A 1 169 CYS 169 200 200 CYS CYS A . n A 1 170 PRO 170 201 201 PRO PRO A . n A 1 171 ASP 171 202 202 ASP ASP A . n A 1 172 GLY 172 203 203 GLY GLY A . n A 1 173 PHE 173 204 204 PHE PHE A . n A 1 174 HIS 174 205 205 HIS HIS A . n A 1 175 GLY 175 206 206 GLY GLY A . n A 1 176 PRO 176 207 207 PRO PRO A . n A 1 177 HIS 177 208 208 HIS HIS A . n A 1 178 CYS 178 209 209 CYS CYS A . n A 1 179 GLU 179 210 210 GLU GLU A . n A 1 180 GLY 180 211 211 GLY GLY A . n A 1 181 THR 181 212 212 THR THR A . n A 1 182 LYS 182 213 ? ? ? A . n A 1 183 HIS 183 214 ? ? ? A . n A 1 184 HIS 184 215 ? ? ? A . n A 1 185 HIS 185 216 ? ? ? A . n A 1 186 HIS 186 217 ? ? ? A . n A 1 187 HIS 187 218 ? ? ? A . n A 1 188 HIS 188 219 ? ? ? A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 PCF 1 1213 1213 PCF PCF A . C 3 NAG 1 1214 1214 NAG NAG A . D 4 CA 1 1215 1215 CA CA A . E 5 SPD 1 1216 1216 SPD SPD A . F 6 HOH 1 2001 2001 HOH HOH A . F 6 HOH 2 2002 2002 HOH HOH A . F 6 HOH 3 2003 2003 HOH HOH A . F 6 HOH 4 2004 2004 HOH HOH A . F 6 HOH 5 2005 2005 HOH HOH A . F 6 HOH 6 2006 2006 HOH HOH A . F 6 HOH 7 2007 2007 HOH HOH A . F 6 HOH 8 2008 2008 HOH HOH A . F 6 HOH 9 2009 2009 HOH HOH A . F 6 HOH 10 2010 2010 HOH HOH A . F 6 HOH 11 2011 2011 HOH HOH A . F 6 HOH 12 2012 2012 HOH HOH A . F 6 HOH 13 2013 2013 HOH HOH A . F 6 HOH 14 2014 2014 HOH HOH A . F 6 HOH 15 2015 2015 HOH HOH A . F 6 HOH 16 2016 2016 HOH HOH A . F 6 HOH 17 2017 2017 HOH HOH A . F 6 HOH 18 2018 2018 HOH HOH A . F 6 HOH 19 2019 2019 HOH HOH A . F 6 HOH 20 2020 2020 HOH HOH A . F 6 HOH 21 2021 2021 HOH HOH A . F 6 HOH 22 2022 2022 HOH HOH A . F 6 HOH 23 2023 2023 HOH HOH A . F 6 HOH 24 2024 2024 HOH HOH A . F 6 HOH 25 2025 2025 HOH HOH A . F 6 HOH 26 2026 2026 HOH HOH A . F 6 HOH 27 2027 2027 HOH HOH A . F 6 HOH 28 2028 2028 HOH HOH A . F 6 HOH 29 2029 2029 HOH HOH A . F 6 HOH 30 2030 2030 HOH HOH A . F 6 HOH 31 2031 2031 HOH HOH A . F 6 HOH 32 2032 2032 HOH HOH A . F 6 HOH 33 2033 2033 HOH HOH A . F 6 HOH 34 2034 2034 HOH HOH A . F 6 HOH 35 2035 2035 HOH HOH A . F 6 HOH 36 2036 2036 HOH HOH A . F 6 HOH 37 2037 2037 HOH HOH A . F 6 HOH 38 2038 2038 HOH HOH A . F 6 HOH 39 2039 2039 HOH HOH A . F 6 HOH 40 2040 2040 HOH HOH A . F 6 HOH 41 2041 2041 HOH HOH A . F 6 HOH 42 2042 2042 HOH HOH A . F 6 HOH 43 2043 2043 HOH HOH A . F 6 HOH 44 2044 2044 HOH HOH A . F 6 HOH 45 2045 2045 HOH HOH A . F 6 HOH 46 2046 2046 HOH HOH A . F 6 HOH 47 2047 2047 HOH HOH A . F 6 HOH 48 2048 2048 HOH HOH A . F 6 HOH 49 2049 2049 HOH HOH A . F 6 HOH 50 2050 2050 HOH HOH A . F 6 HOH 51 2051 2051 HOH HOH A . F 6 HOH 52 2052 2052 HOH HOH A . F 6 HOH 53 2053 2053 HOH HOH A . F 6 HOH 54 2054 2054 HOH HOH A . F 6 HOH 55 2055 2055 HOH HOH A . F 6 HOH 56 2056 2056 HOH HOH A . F 6 HOH 57 2057 2057 HOH HOH A . F 6 HOH 58 2058 2058 HOH HOH A . F 6 HOH 59 2059 2059 HOH HOH A . F 6 HOH 60 2060 2060 HOH HOH A . F 6 HOH 61 2061 2061 HOH HOH A . F 6 HOH 62 2062 2062 HOH HOH A . F 6 HOH 63 2063 2063 HOH HOH A . F 6 HOH 64 2064 2064 HOH HOH A . F 6 HOH 65 2065 2065 HOH HOH A . F 6 HOH 66 2066 2066 HOH HOH A . F 6 HOH 67 2067 2067 HOH HOH A . F 6 HOH 68 2068 2068 HOH HOH A . F 6 HOH 69 2069 2069 HOH HOH A . F 6 HOH 70 2070 2070 HOH HOH A . F 6 HOH 71 2071 2071 HOH HOH A . F 6 HOH 72 2072 2072 HOH HOH A . F 6 HOH 73 2073 2073 HOH HOH A . F 6 HOH 74 2074 2074 HOH HOH A . F 6 HOH 75 2075 2075 HOH HOH A . F 6 HOH 76 2076 2076 HOH HOH A . F 6 HOH 77 2077 2077 HOH HOH A . F 6 HOH 78 2078 2078 HOH HOH A . F 6 HOH 79 2079 2079 HOH HOH A . F 6 HOH 80 2080 2080 HOH HOH A . F 6 HOH 81 2081 2081 HOH HOH A . F 6 HOH 82 2082 2082 HOH HOH A . F 6 HOH 83 2083 2083 HOH HOH A . F 6 HOH 84 2084 2084 HOH HOH A . F 6 HOH 85 2085 2085 HOH HOH A . F 6 HOH 86 2086 2086 HOH HOH A . F 6 HOH 87 2087 2087 HOH HOH A . F 6 HOH 88 2088 2088 HOH HOH A . F 6 HOH 89 2089 2089 HOH HOH A . F 6 HOH 90 2090 2090 HOH HOH A . F 6 HOH 91 2091 2091 HOH HOH A . F 6 HOH 92 2092 2092 HOH HOH A . F 6 HOH 93 2093 2093 HOH HOH A . F 6 HOH 94 2094 2094 HOH HOH A . F 6 HOH 95 2095 2095 HOH HOH A . F 6 HOH 96 2096 2096 HOH HOH A . F 6 HOH 97 2097 2097 HOH HOH A . F 6 HOH 98 2098 2098 HOH HOH A . F 6 HOH 99 2099 2099 HOH HOH A . F 6 HOH 100 2100 2100 HOH HOH A . F 6 HOH 101 2101 2101 HOH HOH A . F 6 HOH 102 2102 2102 HOH HOH A . F 6 HOH 103 2103 2103 HOH HOH A . F 6 HOH 104 2104 2104 HOH HOH A . F 6 HOH 105 2105 2105 HOH HOH A . F 6 HOH 106 2106 2106 HOH HOH A . F 6 HOH 107 2107 2107 HOH HOH A . F 6 HOH 108 2108 2108 HOH HOH A . F 6 HOH 109 2109 2109 HOH HOH A . F 6 HOH 110 2110 2110 HOH HOH A . F 6 HOH 111 2111 2111 HOH HOH A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A ASN 57 A ASN 88 ? ASN 'GLYCOSYLATION SITE' 2 A MLY 31 A MLY 62 ? LYS N-DIMETHYL-LYSINE 3 A MLY 41 A MLY 72 ? LYS N-DIMETHYL-LYSINE 4 A MLY 80 A MLY 111 ? LYS N-DIMETHYL-LYSINE 5 A MLY 99 A MLY 130 ? LYS N-DIMETHYL-LYSINE 6 A MLY 112 A MLY 143 ? LYS N-DIMETHYL-LYSINE 7 A MLY 135 A MLY 166 ? LYS N-DIMETHYL-LYSINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 6220 ? 1 MORE -52.4 ? 1 'SSA (A^2)' 19210 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_455 -x-1,-y,z -1.0000000000 0.0000000000 0.0000000000 -50.7600000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2011-07-13 2 'Structure model' 1 1 2011-08-17 3 'Structure model' 1 2 2020-07-29 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 3 'Structure model' repository Remediation 'Carbohydrate remediation' ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Derived calculations' 4 3 'Structure model' Other 5 3 'Structure model' 'Structure summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp 2 3 'Structure model' entity 3 3 'Structure model' pdbx_chem_comp_identifier 4 3 'Structure model' pdbx_database_status 5 3 'Structure model' pdbx_entity_nonpoly 6 3 'Structure model' struct_conn 7 3 'Structure model' struct_site 8 3 'Structure model' struct_site_gen # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_chem_comp.name' 2 3 'Structure model' '_chem_comp.type' 3 3 'Structure model' '_entity.pdbx_description' 4 3 'Structure model' '_pdbx_database_status.status_code_sf' 5 3 'Structure model' '_pdbx_entity_nonpoly.name' 6 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 7 3 'Structure model' '_struct_conn.pdbx_role' # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x -6.8842 _pdbx_refine_tls.origin_y -13.2750 _pdbx_refine_tls.origin_z 14.9040 _pdbx_refine_tls.T[1][1] 0.1811 _pdbx_refine_tls.T[2][2] 0.2028 _pdbx_refine_tls.T[3][3] 0.1779 _pdbx_refine_tls.T[1][2] -0.0042 _pdbx_refine_tls.T[1][3] -0.0173 _pdbx_refine_tls.T[2][3] 0.0020 _pdbx_refine_tls.L[1][1] 0.7809 _pdbx_refine_tls.L[2][2] 0.4618 _pdbx_refine_tls.L[3][3] 0.7642 _pdbx_refine_tls.L[1][2] 0.3848 _pdbx_refine_tls.L[1][3] 0.1523 _pdbx_refine_tls.L[2][3] -0.2585 _pdbx_refine_tls.S[1][1] -0.0362 _pdbx_refine_tls.S[1][2] -0.0262 _pdbx_refine_tls.S[1][3] 0.1149 _pdbx_refine_tls.S[2][1] 0.0060 _pdbx_refine_tls.S[2][2] 0.0385 _pdbx_refine_tls.S[2][3] 0.0930 _pdbx_refine_tls.S[3][1] -0.1032 _pdbx_refine_tls.S[3][2] -0.0672 _pdbx_refine_tls.S[3][3] -0.0008 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id ? _pdbx_refine_tls_group.beg_auth_seq_id ? _pdbx_refine_tls_group.beg_label_asym_id ? _pdbx_refine_tls_group.beg_label_seq_id ? _pdbx_refine_tls_group.end_auth_asym_id ? _pdbx_refine_tls_group.end_auth_seq_id ? _pdbx_refine_tls_group.end_label_asym_id ? _pdbx_refine_tls_group.end_label_seq_id ? _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.selection_details ALL # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal PHENIX refinement '(PHENIX.REFINE)' ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 PHASER phasing . ? 4 # _pdbx_entry_details.entry_id 2YGP _pdbx_entry_details.compound_details 'ENGINEERED RESIDUE IN CHAIN A, MET 77 TO TRP' _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;ISOFORM Q166K. THE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) AND C-TERMINAL NINE AMINO ACID RESIDUES (GTKHHHHHH) OF THE CRYSTALLISATION CONSTRUCT ARE DERIVED FROM THE PHLSEC VECTOR, CONTAINS MET77TRP MUTATION. ; _pdbx_entry_details.has_ligand_of_interest ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 ND2 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 ASN _pdbx_validate_close_contact.auth_seq_id_1 88 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O5 _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 NAG _pdbx_validate_close_contact.auth_seq_id_2 1214 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.14 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 ALA A 94 ? ? -63.30 1.24 2 1 PRO A 201 ? ? -76.85 -162.11 3 1 ASP A 202 ? ? -40.02 109.85 4 1 CYS A 209 ? ? 62.41 64.17 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A GLU 32 ? A GLU 1 2 1 Y 1 A LYS 213 ? A LYS 182 3 1 Y 1 A HIS 214 ? A HIS 183 4 1 Y 1 A HIS 215 ? A HIS 184 5 1 Y 1 A HIS 216 ? A HIS 185 6 1 Y 1 A HIS 217 ? A HIS 186 7 1 Y 1 A HIS 218 ? A HIS 187 8 1 Y 1 A HIS 219 ? A HIS 188 # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier NAG 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpNAcb NAG 'COMMON NAME' GMML 1.0 N-acetyl-b-D-glucopyranosamine NAG 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-GlcpNAc NAG 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 GlcNAc # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE PCF 3 2-acetamido-2-deoxy-beta-D-glucopyranose NAG 4 'CALCIUM ION' CA 5 SPERMIDINE SPD 6 water HOH #